Conventionally, there is known molecular simulation based on a molecular dynamics method as a methodology of pursuing a phenomenon of entire quantum mechanics using computing machines on the basis of classical dynamics, quantum mechanics or the like. Molecular simulation enables elucidating at the molecular level physical properties of materials such as molecular potential energy, the most stabilized structure, or the like.
There has been introduced no method of arranging atoms in a complicated structure, an ordinary machine structure or the like because the molecular simulation has mainly been used for presumed physical properties of materials. A finite element method is an example of methods of modeling and calculating the complicated structure after dividing it to finite regions. In the case of two-dimensional calculations, there may be a case where a program for generating a mesh is used in order to thoroughly divide an object with triangle or quadrangular regions (see, for example, Patent Document 1).    [Patent Document 1] Japanese Unexamined Patent Application Publication No. 2001-67495